I've been thinking about this a lot so here are my thoughts
Twilight-Ravenclaw because she is so smart, although she could be like Hermione And be in Griffindor
Applejack- Hufflepuff because they are kind, loyal and hard working
Fluttershy- Also Hufflepuff, mostly because of the 'kindness' thing
Rainbow dash- Gryffindor, they are brave, chivalrous, and have strong wills
Pinkie Pie-the hardest for me to place, I think I finally settled on Ravenclaw because they are witty, accepting and unique. Very unique. Remember Luna Lovegood?
Rarity- rarity was honestly almost as hard as pinkie for me, though mostly just between two houses. She is creative like Ravenclaw and ambitious like slytherin, who are in no way any more evil than the other houses. In the end I placed her cunning resourcefulness in slytherin.